AutoCloner

Multiple sequence alignment - TraesCS7B01G269600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS7B01G269600	chr7B	100.000	2594	0	0	1	2594	494433782	494436375	0.000000e+00	4791
1	TraesCS7B01G269600	chr7D	95.396	1564	40	14	568	2114	470836988	470838536	0.000000e+00	2460
2	TraesCS7B01G269600	chr7D	92.998	457	23	5	2143	2594	470838536	470838988	0.000000e+00	658
3	TraesCS7B01G269600	chr7A	88.436	2084	123	49	567	2594	527996367	527994346	0.000000e+00	2405
4	TraesCS7B01G269600	chr7A	88.704	540	31	10	1	536	708389448	708388935	1.310000e-177	632
5	TraesCS7B01G269600	chr4A	93.134	568	29	4	1	559	708997523	708998089	0.000000e+00	824
6	TraesCS7B01G269600	chr4A	87.931	464	39	7	113	562	250526903	250526443	4.920000e-147	531
7	TraesCS7B01G269600	chr2B	92.456	570	35	2	1	562	287782073	287781504	0.000000e+00	808
8	TraesCS7B01G269600	chr2B	92.105	570	36	3	1	562	739957135	739957703	0.000000e+00	795
9	TraesCS7B01G269600	chrUn	90.787	597	19	17	1	562	70454607	70454012	0.000000e+00	765
10	TraesCS7B01G269600	chrUn	88.667	600	28	18	1	562	333484349	333484946	0.000000e+00	695
11	TraesCS7B01G269600	chrUn	88.333	600	30	21	1	562	333487117	333487714	0.000000e+00	684
12	TraesCS7B01G269600	chrUn	89.522	544	46	6	1	536	264216546	264217086	0.000000e+00	678
13	TraesCS7B01G269600	chrUn	87.205	508	53	8	38	536	75000041	75000545	3.750000e-158	568
14	TraesCS7B01G269600	chrUn	86.957	506	56	6	38	536	75403055	75403557	6.270000e-156	560
15	TraesCS7B01G269600	chrUn	92.833	293	11	3	278	562	381044368	381044078	1.440000e-112	416
16	TraesCS7B01G269600	chrUn	91.809	293	14	4	278	562	357069484	357069194	1.450000e-107	399
17	TraesCS7B01G269600	chrUn	91.603	262	14	2	308	562	42846041	42846301	3.170000e-94	355
18	TraesCS7B01G269600	chr5A	90.993	544	36	8	1	536	52002236	52002774	0.000000e+00	721
19	TraesCS7B01G269600	chr3B	89.149	599	28	8	1	562	106068855	106068257	0.000000e+00	712
20	TraesCS7B01G269600	chr3B	84.164	562	70	11	1004	1551	188877217	188877773	6.360000e-146	527
21	TraesCS7B01G269600	chr1B	85.000	600	28	19	1	562	35568159	35568734	1.050000e-153	553
22	TraesCS7B01G269600	chr3D	84.342	562	69	12	1004	1551	132275121	132275677	1.370000e-147	532
23	TraesCS7B01G269600	chr3A	84.164	562	70	11	1004	1551	145667235	145667791	6.360000e-146	527
24	TraesCS7B01G269600	chr4B	93.836	292	11	1	278	562	659326601	659326892	1.430000e-117	433
25	TraesCS7B01G269600	chr1D	93.836	292	10	2	278	562	19576611	19576321	1.430000e-117	433

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS7B01G269600	chr7B	494433782	494436375	2593	False	4791.0	4791	100.000	1	2594	1	chr7B.!!$F1	2593
1	TraesCS7B01G269600	chr7D	470836988	470838988	2000	False	1559.0	2460	94.197	568	2594	2	chr7D.!!$F1	2026
2	TraesCS7B01G269600	chr7A	527994346	527996367	2021	True	2405.0	2405	88.436	567	2594	1	chr7A.!!$R1	2027
3	TraesCS7B01G269600	chr7A	708388935	708389448	513	True	632.0	632	88.704	1	536	1	chr7A.!!$R2	535
4	TraesCS7B01G269600	chr4A	708997523	708998089	566	False	824.0	824	93.134	1	559	1	chr4A.!!$F1	558
5	TraesCS7B01G269600	chr2B	287781504	287782073	569	True	808.0	808	92.456	1	562	1	chr2B.!!$R1	561
6	TraesCS7B01G269600	chr2B	739957135	739957703	568	False	795.0	795	92.105	1	562	1	chr2B.!!$F1	561
7	TraesCS7B01G269600	chrUn	70454012	70454607	595	True	765.0	765	90.787	1	562	1	chrUn.!!$R1	561
8	TraesCS7B01G269600	chrUn	333484349	333487714	3365	False	689.5	695	88.500	1	562	2	chrUn.!!$F5	561
9	TraesCS7B01G269600	chrUn	264216546	264217086	540	False	678.0	678	89.522	1	536	1	chrUn.!!$F4	535
10	TraesCS7B01G269600	chrUn	75000041	75000545	504	False	568.0	568	87.205	38	536	1	chrUn.!!$F2	498
11	TraesCS7B01G269600	chrUn	75403055	75403557	502	False	560.0	560	86.957	38	536	1	chrUn.!!$F3	498
12	TraesCS7B01G269600	chr5A	52002236	52002774	538	False	721.0	721	90.993	1	536	1	chr5A.!!$F1	535
13	TraesCS7B01G269600	chr3B	106068257	106068855	598	True	712.0	712	89.149	1	562	1	chr3B.!!$R1	561
14	TraesCS7B01G269600	chr3B	188877217	188877773	556	False	527.0	527	84.164	1004	1551	1	chr3B.!!$F1	547
15	TraesCS7B01G269600	chr1B	35568159	35568734	575	False	553.0	553	85.000	1	562	1	chr1B.!!$F1	561
16	TraesCS7B01G269600	chr3D	132275121	132275677	556	False	532.0	532	84.342	1004	1551	1	chr3D.!!$F1	547
17	TraesCS7B01G269600	chr3A	145667235	145667791	556	False	527.0	527	84.164	1004	1551	1	chr3A.!!$F1	547

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
264	297	0.032017	TAGGAGCAGGAGGAAGGACC	60.032	60.0	0.0	0.0	39.35	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1895	4822	1.351017	CAGCTACCTGAGTTTTCCCCA	59.649	52.381	0.0	0.0	41.77	4.96	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	2.482414	ATCCGACCCCTATTGGTACA	57.518	50.000	0.00	0.00	39.24	2.90
91	93	2.531206	CTAGGCACTTACAGCGAAGAC	58.469	52.381	3.47	0.00	41.75	3.01
174	177	3.839432	GTCCGCTCGGGGAAGGAG	61.839	72.222	8.59	0.00	37.96	3.69
178	181	4.798682	GCTCGGGGAAGGAGGGGA	62.799	72.222	0.00	0.00	32.10	4.81
179	182	2.444895	CTCGGGGAAGGAGGGGAG	60.445	72.222	0.00	0.00	0.00	4.30
180	183	4.089757	TCGGGGAAGGAGGGGAGG	62.090	72.222	0.00	0.00	0.00	4.30
182	185	4.439901	GGGGAAGGAGGGGAGGCT	62.440	72.222	0.00	0.00	0.00	4.58
183	186	2.770475	GGGAAGGAGGGGAGGCTC	60.770	72.222	5.78	5.78	0.00	4.70
184	187	3.157949	GGAAGGAGGGGAGGCTCG	61.158	72.222	8.69	0.00	0.00	5.03
185	188	2.364448	GAAGGAGGGGAGGCTCGT	60.364	66.667	8.69	0.00	0.00	4.18
186	189	2.364448	AAGGAGGGGAGGCTCGTC	60.364	66.667	8.69	5.06	0.00	4.20
187	190	4.824515	AGGAGGGGAGGCTCGTCG	62.825	72.222	8.69	0.00	0.00	5.12
189	192	4.816984	GAGGGGAGGCTCGTCGGA	62.817	72.222	8.69	0.00	0.00	4.55
190	193	4.377760	AGGGGAGGCTCGTCGGAA	62.378	66.667	8.69	0.00	0.00	4.30
263	296	1.116308	GTAGGAGCAGGAGGAAGGAC	58.884	60.000	0.00	0.00	0.00	3.85
264	297	0.032017	TAGGAGCAGGAGGAAGGACC	60.032	60.000	0.00	0.00	39.35	4.46
366	3226	4.533222	ACCAAATTTCAAAAGAGTACGCG	58.467	39.130	3.53	3.53	0.00	6.01
505	3366	3.056107	GGTCAAAAATACCCTTGGGCTTC	60.056	47.826	5.46	0.00	0.00	3.86
564	3433	6.903883	ACACGTGATTTGGTGTATTATCTC	57.096	37.500	25.01	0.00	44.98	2.75
565	3434	5.815740	ACACGTGATTTGGTGTATTATCTCC	59.184	40.000	25.01	0.00	44.98	3.71
623	3494	2.158784	ACCAAACGCACCTTACAACCTA	60.159	45.455	0.00	0.00	0.00	3.08
721	3600	1.081242	CACGCTGGCACCAATTCAC	60.081	57.895	0.00	0.00	0.00	3.18
769	3648	1.102978	AAAAGTTGCTGCTTGTCGGT	58.897	45.000	0.00	0.00	0.00	4.69
781	3660	2.746269	CTTGTCGGTTTCCTCGTAACA	58.254	47.619	0.00	0.00	0.00	2.41
808	3688	2.253513	GCTAGCTAGCTCTCCCTCG	58.746	63.158	33.71	1.74	45.62	4.63
809	3689	1.241315	GCTAGCTAGCTCTCCCTCGG	61.241	65.000	33.71	1.21	45.62	4.63
1600	4503	1.649815	CGGCGCGACTAGAAGAGAT	59.350	57.895	12.10	0.00	0.00	2.75
1606	4514	2.032377	CGCGACTAGAAGAGATGAGACC	60.032	54.545	0.00	0.00	0.00	3.85
1610	4518	4.878971	CGACTAGAAGAGATGAGACCAGAA	59.121	45.833	0.00	0.00	0.00	3.02
1614	4522	3.701040	AGAAGAGATGAGACCAGAAGAGC	59.299	47.826	0.00	0.00	0.00	4.09
1694	4609	1.541670	GCCGTGGTTGTTAGTTGGAGA	60.542	52.381	0.00	0.00	0.00	3.71
1695	4610	2.140717	CCGTGGTTGTTAGTTGGAGAC	58.859	52.381	0.00	0.00	0.00	3.36
1696	4611	2.224209	CCGTGGTTGTTAGTTGGAGACT	60.224	50.000	0.00	0.00	42.55	3.24
1697	4612	3.463944	CGTGGTTGTTAGTTGGAGACTT	58.536	45.455	0.00	0.00	39.86	3.01
1698	4613	3.247648	CGTGGTTGTTAGTTGGAGACTTG	59.752	47.826	0.00	0.00	39.86	3.16
1699	4614	3.564225	GTGGTTGTTAGTTGGAGACTTGG	59.436	47.826	0.00	0.00	39.86	3.61
1718	4633	2.758423	TGGAGTACTCTGCTATTTCGCA	59.242	45.455	21.88	5.07	38.40	5.10
2006	4934	7.307396	CCGCGAATACAATAATGTTCTCATTCT	60.307	37.037	8.23	0.00	42.45	2.40
2022	4950	6.545508	TCTCATTCTAATCAATGTGCAAACG	58.454	36.000	0.00	0.00	35.56	3.60
2023	4951	5.639757	TCATTCTAATCAATGTGCAAACGG	58.360	37.500	0.00	0.00	35.56	4.44
2064	4992	7.597327	ACTAGATCCTCAGTAGTAATTCCCTT	58.403	38.462	0.00	0.00	0.00	3.95
2115	5044	5.712917	GGCATCCTAGATTGCTAGTACTAGT	59.287	44.000	26.76	10.94	42.11	2.57
2116	5045	6.885376	GGCATCCTAGATTGCTAGTACTAGTA	59.115	42.308	26.76	21.67	42.11	1.82
2121	5061	9.947433	TCCTAGATTGCTAGTACTAGTAAGATC	57.053	37.037	29.28	23.92	42.11	2.75
2136	5076	5.402398	AGTAAGATCGAAATTGCAAAAGCC	58.598	37.500	1.71	0.00	0.00	4.35
2137	5077	2.867429	AGATCGAAATTGCAAAAGCCG	58.133	42.857	1.71	5.40	0.00	5.52
2138	5078	2.228822	AGATCGAAATTGCAAAAGCCGT	59.771	40.909	1.71	0.00	0.00	5.68
2139	5079	2.500509	TCGAAATTGCAAAAGCCGTT	57.499	40.000	1.71	0.00	0.00	4.44
2140	5080	2.389998	TCGAAATTGCAAAAGCCGTTC	58.610	42.857	1.71	0.17	0.00	3.95
2141	5081	1.455408	CGAAATTGCAAAAGCCGTTCC	59.545	47.619	1.71	0.00	0.00	3.62
2142	5082	2.478831	GAAATTGCAAAAGCCGTTCCA	58.521	42.857	1.71	0.00	0.00	3.53
2160	5100	6.273071	CGTTCCATCCCCATTTTAGAAAATC	58.727	40.000	0.00	0.00	36.52	2.17
2171	5111	4.875544	TTTAGAAAATCAGGCGATTCCG	57.124	40.909	5.33	0.00	41.12	4.30
2209	5149	6.257849	CACTAGCAGGATCAACGCTAATTAAA	59.742	38.462	10.16	0.00	37.77	1.52
2211	5151	6.699575	AGCAGGATCAACGCTAATTAAATT	57.300	33.333	1.29	0.00	33.25	1.82
2215	5155	7.587757	GCAGGATCAACGCTAATTAAATTGTAG	59.412	37.037	0.00	0.00	0.00	2.74
2300	5241	1.756561	AAAAGCAGTGGCCACCGTT	60.757	52.632	32.29	18.18	42.56	4.44
2319	5260	0.888736	TTCTTGCTAGCCAAAGCGCA	60.889	50.000	13.29	0.00	45.85	6.09
2349	5300	7.167816	ACTTATAAAAGAGCAAGCGGCATGG	62.168	44.000	7.37	0.00	39.62	3.66
2400	5351	0.545548	AAAGCTTCTCCGGGAGAGGT	60.546	55.000	29.88	23.11	43.44	3.85
2408	5359	2.357517	CGGGAGAGGTGTGTGCAC	60.358	66.667	10.75	10.75	44.53	4.57
2440	5392	0.616371	CGGTGGTGACCAGGGAATAA	59.384	55.000	3.58	0.00	43.33	1.40
2527	5479	3.399330	TCATGGGTCTCACGACTTTTTC	58.601	45.455	0.00	0.00	40.10	2.29
2528	5480	2.249844	TGGGTCTCACGACTTTTTCC	57.750	50.000	0.00	0.00	40.10	3.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	3.951563	TGCTGGTCCCTTATGCTTATT	57.048	42.857	0.00	0.00	0.00	1.40
91	93	0.596082	ATCAACTTTTTCACGCCGGG	59.404	50.000	2.18	0.00	0.00	5.73
172	175	4.816984	TCCGACGAGCCTCCCCTC	62.817	72.222	0.00	0.00	0.00	4.30
173	176	4.377760	TTCCGACGAGCCTCCCCT	62.378	66.667	0.00	0.00	0.00	4.79
174	177	3.839432	CTTCCGACGAGCCTCCCC	61.839	72.222	0.00	0.00	0.00	4.81
175	178	2.077821	GATCTTCCGACGAGCCTCCC	62.078	65.000	0.00	0.00	0.00	4.30
176	179	1.104577	AGATCTTCCGACGAGCCTCC	61.105	60.000	0.00	0.00	0.00	4.30
177	180	0.030101	CAGATCTTCCGACGAGCCTC	59.970	60.000	0.00	0.00	0.00	4.70
178	181	1.388065	CCAGATCTTCCGACGAGCCT	61.388	60.000	0.00	0.00	0.00	4.58
179	182	1.066587	CCAGATCTTCCGACGAGCC	59.933	63.158	0.00	0.00	0.00	4.70
180	183	1.590259	GCCAGATCTTCCGACGAGC	60.590	63.158	0.00	0.00	0.00	5.03
181	184	1.298713	CGCCAGATCTTCCGACGAG	60.299	63.158	6.00	0.00	0.00	4.18
182	185	2.798689	CGCCAGATCTTCCGACGA	59.201	61.111	6.00	0.00	0.00	4.20
183	186	2.956964	GCGCCAGATCTTCCGACG	60.957	66.667	14.18	5.79	0.00	5.12
184	187	2.586357	GGCGCCAGATCTTCCGAC	60.586	66.667	24.80	8.61	0.00	4.79
185	188	4.207281	CGGCGCCAGATCTTCCGA	62.207	66.667	28.98	0.00	42.43	4.55
188	191	4.873129	TCGCGGCGCCAGATCTTC	62.873	66.667	28.98	4.64	0.00	2.87
264	297	1.631072	GATCGCAATCACCGTGTCG	59.369	57.895	0.00	0.00	31.76	4.35
366	3226	5.724328	TCATTATAGAGGTCCAATCATCGC	58.276	41.667	0.00	0.00	0.00	4.58
425	3285	2.172717	CCAGGGGTATTCTCGTCCAAAT	59.827	50.000	0.00	0.00	0.00	2.32
505	3366	5.221048	CGGATTAGAATAACTGGGCCTTTTG	60.221	44.000	4.53	0.00	0.00	2.44
562	3431	5.531659	TCTCGCTAAGTATTTGACTAGGGAG	59.468	44.000	13.08	13.08	42.42	4.30
563	3432	5.443283	TCTCGCTAAGTATTTGACTAGGGA	58.557	41.667	0.00	0.00	37.44	4.20
564	3433	5.769484	TCTCGCTAAGTATTTGACTAGGG	57.231	43.478	0.00	0.00	37.44	3.53
565	3434	7.539366	GCTTATCTCGCTAAGTATTTGACTAGG	59.461	40.741	0.00	0.00	37.44	3.02
623	3494	1.227556	GTTGTGTCAGTGGGCGAGT	60.228	57.895	0.00	0.00	0.00	4.18
721	3600	3.334691	ACGATTGTTGTGGTACAGATGG	58.665	45.455	0.00	0.00	41.80	3.51
769	3648	2.023223	GGCGCGTGTTACGAGGAAA	61.023	57.895	8.43	0.00	46.05	3.13
870	3750	5.665812	GGATGGCTGGGATGGTTATATACTA	59.334	44.000	0.00	0.00	0.00	1.82
1031	3922	4.400251	CCTCCGTCACCCCCTCCT	62.400	72.222	0.00	0.00	0.00	3.69
1587	4490	4.447290	TCTGGTCTCATCTCTTCTAGTCG	58.553	47.826	0.00	0.00	0.00	4.18
1600	4503	1.599606	GGAGCGCTCTTCTGGTCTCA	61.600	60.000	34.46	0.00	33.30	3.27
1678	4589	3.456644	TCCAAGTCTCCAACTAACAACCA	59.543	43.478	0.00	0.00	37.17	3.67
1694	4609	4.678309	GCGAAATAGCAGAGTACTCCAAGT	60.678	45.833	19.38	4.71	37.05	3.16
1695	4610	3.799420	GCGAAATAGCAGAGTACTCCAAG	59.201	47.826	19.38	10.79	37.05	3.61
1696	4611	3.194755	TGCGAAATAGCAGAGTACTCCAA	59.805	43.478	19.38	3.05	42.92	3.53
1697	4612	2.758423	TGCGAAATAGCAGAGTACTCCA	59.242	45.455	19.38	3.31	42.92	3.86
1698	4613	3.438297	TGCGAAATAGCAGAGTACTCC	57.562	47.619	19.38	5.15	42.92	3.85
1718	4633	5.755409	AACAAACAGAAAAGGAAAAGGGT	57.245	34.783	0.00	0.00	0.00	4.34
1895	4822	1.351017	CAGCTACCTGAGTTTTCCCCA	59.649	52.381	0.00	0.00	41.77	4.96
2006	4934	5.635417	TCAATCCGTTTGCACATTGATTA	57.365	34.783	0.00	0.00	35.16	1.75
2022	4950	2.206576	AGTTCCCAGCTGTTCAATCC	57.793	50.000	13.81	0.00	0.00	3.01
2023	4951	4.207891	TCTAGTTCCCAGCTGTTCAATC	57.792	45.455	13.81	0.00	0.00	2.67
2031	4959	2.023501	ACTGAGGATCTAGTTCCCAGCT	60.024	50.000	24.17	15.42	37.48	4.24
2136	5076	5.652994	TTTTCTAAAATGGGGATGGAACG	57.347	39.130	0.00	0.00	0.00	3.95
2137	5077	7.181569	TGATTTTCTAAAATGGGGATGGAAC	57.818	36.000	5.44	0.00	38.64	3.62
2138	5078	6.383726	CCTGATTTTCTAAAATGGGGATGGAA	59.616	38.462	5.44	0.00	38.64	3.53
2139	5079	5.898972	CCTGATTTTCTAAAATGGGGATGGA	59.101	40.000	5.44	0.00	38.64	3.41
2140	5080	5.453762	GCCTGATTTTCTAAAATGGGGATGG	60.454	44.000	5.44	1.24	38.64	3.51
2141	5081	5.604565	GCCTGATTTTCTAAAATGGGGATG	58.395	41.667	5.44	0.00	38.64	3.51
2142	5082	4.342092	CGCCTGATTTTCTAAAATGGGGAT	59.658	41.667	5.44	0.00	38.64	3.85
2160	5100	2.076863	GGGATTATTCGGAATCGCCTG	58.923	52.381	6.49	0.00	40.89	4.85
2171	5111	4.528596	TCCTGCTAGTGCTAGGGATTATTC	59.471	45.833	8.16	0.00	40.48	1.75
2215	5155	5.978322	GCTCAACCAATAGTAGTAGCTGTAC	59.022	44.000	0.00	0.00	0.00	2.90
2219	5160	3.952323	TCGCTCAACCAATAGTAGTAGCT	59.048	43.478	0.00	0.00	0.00	3.32
2226	5167	4.156008	GGTCAAATTCGCTCAACCAATAGT	59.844	41.667	0.00	0.00	0.00	2.12
2300	5241	0.888736	TGCGCTTTGGCTAGCAAGAA	60.889	50.000	18.24	6.76	41.28	2.52
2319	5260	2.985896	TGCTCTTTTATAAGTGGCGCT	58.014	42.857	7.64	0.00	35.57	5.92
2400	5351	2.321333	CGGGCGTATTGTGCACACA	61.321	57.895	21.56	11.57	39.98	3.72
2429	5380	1.844497	GCTACCCAGTTATTCCCTGGT	59.156	52.381	5.78	0.00	46.68	4.00
2440	5392	1.550976	GTTAGTCAGCTGCTACCCAGT	59.449	52.381	9.47	0.00	43.71	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.